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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac...

Basic information

species Zea mays
transcript GRMZM2G368908_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 3
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac-----
||||||||||||||||||||||||||||||| || |||||||| |||||||| ||||||||| | || ||| | ||||| | || ||          |||     |||| |||| |  || |  |    ||| | |||| |    |    |    |     ||| ||      ||   |||      
CCAAGGAGCATGTTGTTGGCTGGTACAGCACCGGTCCAAAACTCAGGGAGAACGACTTGGATATACACGCACTATTCAATAAgtatgtgatgtaccgaagct---ttatatcctgtattgttcatgaagttatattcttgactagatatgttgttttggtgcaagtaatct--ttattaaattgtct

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggt--------gaacctgcaagtg--aagttatgtcctcttatggtt----gttcttttaaactcttaatacaacccctga---gctatagacaaatatgtaaatttccaaac-------------------------------------------------------------------
|||||||||||||||| || ||||||||||| ||||| |||||  | |||||||| |||||||| || || ||||||||  |||  | |         | | | ||  |   || | ||   |  |||||| |    | |||| |      | |||         ||   | | ||| |  | || |   ||||    |                                                                   
CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGGgttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 5'ss of exon 3
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtg---gtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac
||||||||||||||||||| ||||| ||||| || ||||||||  ||||||||||  | ||| | ||   | | ||| |   ||| |    | ||  |  |     |   |||   | |||  |    |   |   | |||  | | |||   |   | |  || |  | ||| ||  | ||   
CCAAGGAGCATGTTGTTGGTTGGTATAGCACAGGACCAAAACTGCGGGAGAATGATCTAGATATTCACAGACTATTCCATGAgtgagctcattaatttttattcttataaatgatgtgttaatgaaacttaatcttattctggaaaaaactgtttttcaactgatatgtttgtgaagcttca---

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 3
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtg---gtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac
|||||||||| || ||||| ||||||||||| || ||||||||  ||||||||||| | ||| | || | | ||||| |   ||  |    || | ||  |     |   | |     |||  |   ||   |   | |||  | |       |  || |  || | ||  || ||  |  |   
CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgattaattactgaaatttaatcttattctgga-aagcttattttgcaactgatatattagtgaagcttgat--

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ23777 (Selaginella moellendorffii), 5'ss of exon 3
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac
| |||||||| |||||||| |||||||||||||| || |||||| | ||||| ||  | ||  | || |   | || |  | ||| |   ||  ||    |     ||| |  |||| ||| |  | | ||   |  ||     |   | |   | |                         
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgaga--aatttgtttct----ctat-ttttcttctggattctatcttgctcatttgtgtgattgcttctaccag------------------------

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac
| |||||||| |||||||| |||||||||||||| || |||||| | ||||| ||  | ||  | || |   | || |  | ||| |   |   ||    |    |  | |  | || || ||| || |||      |||   | |||                                  
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgaga-aattttgtttctctcttcttctttttttctgtttgctcatttgtgtgattacgtctaccag--------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|149042715|gb|EE047230.2|EE047230
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
EST: gi|88755238|gb|DY539379.1|DY539379
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
EST: gi|32930134|gb|CF034946.1|CF034946
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
EST: gi|71301807|gb|DR786975.1|DR786975
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTC
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTC
EST: gi|211163165|gb|FL410935.1|FL410935
EST:     GGCCCAAAGCTAAGGGAGAATGACTTGGATGTTCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
EST: gi|15208970|gb|BI430854.1|BI430854
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
EST: gi|20507024|gb|BQ279450.1|BQ279450
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGCTCAACAG                         CTATGCTCCTAACCCTGTCCTAG
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAG
EST: gi|148973687|gb|EE024808.2|EE024808
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
EST: gi|26456618|gb|CA828201.1|CA828201
EST:     GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG                         TTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT
genomic: GGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 170

CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCTTGGGATACCCACCAAGGCGTATTACGCCGTGGAAGAAGTTAAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 211

CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCTTGGGATACCCACCAAGGCGTATTACGCCGTGGAAGAAGTTAAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 165

CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCTTGGGATACCCACCAAGGCGTATTACGCCGTGGAAGAAGTTAAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaa ... caatttgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCTTGGGATACCCACCAAGGCGTATTACGCCGTGGAAGAAGTTAAAGAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac

- - - - - - - - - - - - - - - - - - - - - - - GGAGAA